Earlier in the episode, Jamie tells Murtagh he’s withdrawn the charge (which cancels the duel). Murtagh doesn’t understand why and compares Jamie’s vacillating to a woman in flux. I’m not sure how Murtagh knows so much about this, so I’ll move on
I don’t believe Murtagh really thinks Claire is a witch. He’s probably heard stories of the stones and then listened to the ballads played at Castle Leoch that tell the tale. “You lived through all these years, then,” he says, showing her the paper with the years 1918-1945 on it.
My heart begins to crumble as Murtagh struggles to come to terms with his own mortality. “You know what happens to the Jacobites.” Claire nods. “You know how it ends, and it doesn’t end well,” he continues as he stands to face her. “You know when things will happen, when people will die.” His eyes search hers for answers to questions he’s not yet asked. Perhaps he doesn’t want to know.